Focused ion beam (FIB) irradiation of a thin Ni2Si and NiSi2 layers deposited on a Si substrate was carried out and studied using an in-situ transmission electron microscope (TEM). A set of 3 x 3-mu m squares was patterned at room temperature (RT) with a 25-keV Ga+-FIB attached to the TEM. FIB patterning to Ni2Si/Si sample causes loss of silicide crystallinity. Annealing at 673 K resulted in the precipitation of Ni rich silicide. FIB patterning to NiSi2/Si sample causes fragmentation and produces defects near the irradiated edge. Annealing at 673 K improved silicide film quality.